Editorial: Peptide and protein modifications

The structure-functional property relationship of peptides and proteins plays a determining role in many biological processes. Given the key role that conformation has in defining the physicochemical characteristics of peptides and proteins, there is a growing demand for modifications that alter structure, solubility and other physicochemical properties of these molecules, such as hydrophobicity, hydrophilicity, charge distribution, and particle size. This editorial article summaries the scope and contents of the Special Issue “Peptide and Protein Modifications”, which is associated with Peptide and Protein Metalation Congress, whose first edition was held in Naples, Italy (10–12 June 2025) and whose second edition was scheduled for 2027 (Pisa, Italy, 9–11 June 2027, https://ppm2.dcci.unipi.it/). This Research Topic aimed to explore recent advancements in peptide and protein modifications and their applications in chemical biology. Particular emphasis was devoted to a peculiar form of protein modification: the metalation, i.e., the process by which metal ions or metal complexes coordinate to residue side chains forming metal/peptide or metal/protein adducts. Protein metalation plays a major role for several fundamental physiological processes including homeostasis, metal storage or delivery, protein folding, and is also relevant for function and toxicity of metallodrugs and for the design of artificial metalloenzymes.

This Research Topic contains six contributions, i.e., three perspective articles, two original articles and a brief research report. The papers present new ideas and results or provide overviews and discussions of the existing results in the field of peptide and protein modifications.

The Perspective article entitled “Protein metalation by anticancer metal-based drugs revealed through the integration of ESI-MS and XRD measurements. State of the art and open issues” (Merlino et al.) follows previous works from Merlino et al.(Merlino et al., 2017; Messori and Merlino, 2017; Merlino, 2021) reporting an overview of recent applications of the combined use of X-ray crystallography and mass spectrometry approach to unveil the molecular basis of the recognition of metal compounds of pharmaceutical interest by proteins. This approach has been successful in elucidating metal binding sites and metal-containing fragments bound to small model proteins and proteins of physiological relevance, including albumin (Ferraro et al., 2015), ferritin (Cosottini et al., 2025; Monti et al., 2019; Kasyutich et al., 2010) and transferrin (Troisi et al., 2025a; Troisi et al., 2025b).

Chiaverini et al. explore the role of computational methods and models in complementing experimental data for the elucidation of mechanisms at the basis of the metalation process. The use of complementary computational and experimental modelling strategies is advantageous since it reduces the research costs and allows us to predict the behavior of specific systems under conditions that are not easy to realize in laboratory. The multilevel approach starts with simplified models like residue side chains, but complex systems can also be modelled. Selected examples from literature are reported and discussed. Case studies include SARS-CoV-2 nsp13 metalation by bismuth (III) ions (Tolbatov et al., 2022) and the metalation of nucleophilic sites in proteins by diruthenium and dirhodium paddlewheel complexes (Tolbatov and Marrone, 2022a; Tolbatov and Marrone, 2022b), and by gold complexes auranofin and its analog Au(PEt₃)I (Tolbatov et al., 2020).

The Perspective paper by Gailer discusses the use of proper analytical tools for evaluating toxic metal (loid) species (TMS), in particular mercury and cadmium, in complex matrices near physiological conditions. In particular, he focusses his attention on the use of liquid chromatography (LC) methods, which could be used in the future to address questions regarding the dose-response relationship of other emerging TMS.

The research articles and the brief research report broaden the spectrum of peptide and protein modifications covered in the Research Topic.

Difino et al. report synthesis and structural characterization by X-ray crystallography and nuclear magnetic resonance (NMR) of six new ferrocene (Fc)-peptide conjugates with potential for pharmacological use. Redox properties and stability within human serum of the Fc derivatives were also evaluated. The aim of the work was to study the influence of the linker, and of the length of spacer and peptide on the redox properties of the Fc derivatives. This is relevant since it is known that Fc anti-proliferative activity is linked to its ability to promote the formation of reactive oxygen species (ROS) (Wang and Astruc, 2025). The results of the work demonstrate that the Fc-peptide link plays the major role in bringing the Fc oxidation potential closer to that of physiological environments, while minor modifications are associated with change of the length of the spacer and of the peptide.

The research paper entitled “Reactivity in cell culture medium and in vitro anticancer activity of 3,5di-tert-butylcatechol: link to metal-catechol interactions” (Levina et al.) studies the catechol (1,2-dihydroxybenzene) speciation in biological media, including cell culture media, and the impact that transition metal ions can have on this phenomenon. This impact is crucial, as evidenced by the results reported in the paper. Levina et al. demonstrate, using 3,5-di-tert-butylcatechol (dtbH2) and its oxidation product, 3,5-di-tert-butyl-o-quinone (dtbQ), which show antiproliferative properties against T98G (glioblastoma) and A549 (lung carcinoma) cell lines, that the activity is affected by glutathione (GSH). This work provides a valuable example of the complexity underlying anti-proliferation potency and highlights the importance of studying drug speciation, interaction with GSH and aging in cell culture media (Levina et al., 2017).

The brief research report by Ghosh describes the synthesis of a boronic acid-modified cell-penetrating peptide, cR10B2, which is then conjugated to ubiquitin (Ub). Cell-penetrating peptides are peptides typically rich in Arg or Lys that are used as non-viral delivery systems (Reissmann, 2021). The authors demonstrate that cR10B2 facilitates Ub translocation across cell membranes when compared to the classical cell-penetrating peptide TAT. A similar strategy was used in the past for the delivery of Ub within live U2OS cells (Ghosh, 2024). The derivatization of cell-penetrating peptides with boronic acid is a promising strategy for protein delivery; future works should evaluate the possibility to apply this strategy in a context that can involve clinician therapies.

In conclusion, the six articles published on the Special Issue highlight the strategic use of a combination of experimental and computational approaches to study peptide and protein modifications. The results and the discussion presented in these works suggest that future research in the field of peptide and protein metalation should consider complex biological matrices (starting from a mixture of protein systems) that better mimic the crowded cellular milieu and propose the potential use of multilevel modelling strategy for designing improved next-generation drugs. On the other hand, data reported in the original articles underline the importance of studying speciation of biologically-active metal complexes within physiological conditions and support the strategic use of other peptide and protein structural modifications that can be helpful for improving physico-chemical features of these molecules enhancing their biological properties, their redox behavior, their ability to act as delivery systems. These approaches will open new frontiers for the treatment of human diseases.

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Footnotes

Edited and reviewed by: Isabel Correia, University of Lisbon, Portugal